Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

L.A.F. Frantz, O. Madsen, H.J.W.C. Megens, Y. Paudel, M. Bosse, R.P.M.A. Crooijmans, M. Groenen, J.G. Schraiber

Research output: Contribution to journalArticleAcademicpeer-review

70 Citations (Scopus)

Abstract

Background Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog. Results Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal. Conclusions Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.
LanguageEnglish
Article numberR107
Number of pages12
JournalGenome Biology
Volume14
Issue number9
DOIs
Publication statusPublished - 2013

Fingerprint

Sus
Southeastern Asia
Gene Flow
genome
History
Genome
South East Asia
history
gene flow
Swine
Phacochoerus aethiopicus
loci
Genetic Loci
Phylogeny
Genomics
Islands
pig
translocation
subspecies
genomics

Keywords

  • last glacial period
  • southeast-asia
  • recombination rates
  • complex speciation
  • maximum-likelihood
  • genetic-evidence
  • se asia
  • evolution
  • inference
  • reconstructions

Cite this

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title = "Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus",
abstract = "Background Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog. Results Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal. Conclusions Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.",
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language = "English",
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Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus. / Frantz, L.A.F.; Madsen, O.; Megens, H.J.W.C.; Paudel, Y.; Bosse, M.; Crooijmans, R.P.M.A.; Groenen, M.; Schraiber, J.G.

In: Genome Biology, Vol. 14, No. 9, R107, 2013.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

AU - Frantz, L.A.F.

AU - Madsen, O.

AU - Megens, H.J.W.C.

AU - Paudel, Y.

AU - Bosse, M.

AU - Crooijmans, R.P.M.A.

AU - Groenen, M.

AU - Schraiber, J.G.

PY - 2013

Y1 - 2013

N2 - Background Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog. Results Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal. Conclusions Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.

AB - Background Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog. Results Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal. Conclusions Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.

KW - last glacial period

KW - southeast-asia

KW - recombination rates

KW - complex speciation

KW - maximum-likelihood

KW - genetic-evidence

KW - se asia

KW - evolution

KW - inference

KW - reconstructions

U2 - 10.1186/gb-2013-14-9-r107

DO - 10.1186/gb-2013-14-9-r107

M3 - Article

VL - 14

JO - Genome Biology

T2 - Genome Biology

JF - Genome Biology

SN - 1474-7596

IS - 9

M1 - R107

ER -